def __get_planned_liquid_transfers(self, step_container, transfer_type):
# Create :class:`PlannedSampleDilution`s for dilution (requires
# valid diluent), otherwise it creates
# :class:`PlannedSampleTransfer`s.
planned_liquid_transfers = []
for transfer_container in step_container.get_transfer_containers():
src_positions = transfer_container.get_source_positions()
trg_positions = transfer_container.get_target_positions()
volume = float(transfer_container.volume) / VOLUME_CONVERSION_FACTOR
if transfer_type == TRANSFER_TYPES.SAMPLE_DILUTION:
diluent = transfer_container.diluent
if diluent is None or not len(str(diluent)) > 1:
msg = 'A diluent must be at least 2 characters long! ' \
'Change the diluent for step %i code %s, ' \
'please.' \
% (step_container.number, transfer_container.code)
self.add_error(msg)
return None
for trg_pos_container in trg_positions:
trg_pos = self._convert_to_rack_position(trg_pos_container)
kw = dict(target_position=trg_pos, volume=volume)
if transfer_type == TRANSFER_TYPES.SAMPLE_DILUTION:
kw['diluent_info'] = str(transfer_container.diluent)
psd = PlannedSampleDilution.get_entity(**kw)
planned_liquid_transfers.append(psd)
else:
for src_pos_container in src_positions:
src_pos = self._convert_to_rack_position(
src_pos_container)
kw['source_position'] = src_pos
pst = PlannedSampleTransfer.get_entity(**kw)
planned_liquid_transfers.append(pst)
return planned_liquid_transfers
def _create_planned_liquid_transfers(self):
"""
Generates the planned container dilutions for the worklist.
"""
self.add_debug('Generate planned container dilutions ...')
invalid_dil_factor = dict()
for rack_pos, tf_pos in self.transfection_layout.iterpositions():
if tf_pos.is_empty:
continue
dil_volume = tf_pos.calculate_reagent_dilution_volume() \
/ VOLUME_CONVERSION_FACTOR
ini_dil_factor = TransfectionParameters.\
calculate_initial_reagent_dilution(
float(tf_pos.reagent_dil_factor))
if ini_dil_factor <= 1:
add_list_map_element(invalid_dil_factor,
tf_pos.reagent_dil_factor, rack_pos.label)
continue
rdf_str = get_trimmed_string(tf_pos.reagent_dil_factor)
diluent_info = '%s (%s)' % (tf_pos.reagent_name, rdf_str)
psd = PlannedSampleDilution.get_entity(volume=dil_volume,
target_position=rack_pos,
diluent_info=diluent_info)
self._add_planned_transfer(psd)
if len(invalid_dil_factor) > 0:
msg = 'Invalid dilution reagent factor for rack positions: %s. ' \
'The factor would result in an initial dilution factor of ' \
'less then 1!' % (self._get_joined_map_str(invalid_dil_factor))
self.add_error(msg)
def _create_planned_liquid_transfers(self):
"""
Generates the planned container dilutions for the worklist.
"""
self.add_debug('Generate planned container dilutions ...')
invalid_dil_factor = dict()
for rack_pos, tf_pos in self.transfection_layout.iterpositions():
if tf_pos.is_empty:
continue
dil_volume = tf_pos.calculate_reagent_dilution_volume() \
/ VOLUME_CONVERSION_FACTOR
ini_dil_factor = TransfectionParameters.\
calculate_initial_reagent_dilution(
float(tf_pos.reagent_dil_factor))
if ini_dil_factor <= 1:
add_list_map_element(invalid_dil_factor,
tf_pos.reagent_dil_factor, rack_pos.label)
continue
rdf_str = get_trimmed_string(tf_pos.reagent_dil_factor)
diluent_info = '%s (%s)' % (tf_pos.reagent_name, rdf_str)
psd = PlannedSampleDilution.get_entity(volume=dil_volume,
target_position=rack_pos,
diluent_info=diluent_info)
self._add_planned_transfer(psd)
if len(invalid_dil_factor) > 0:
msg = 'Invalid dilution reagent factor for rack positions: %s. ' \
'The factor would result in an initial dilution factor of ' \
'less then 1!' % (self._get_joined_map_str(invalid_dil_factor))
self.add_error(msg)
def _create_planned_sample_dilution(self, **kw):
if not 'volume' in kw:
kw['volume'] = 0.000020
if not 'target_position' in kw:
kw['target_position'] = self._get_entity(IRackPosition)
if not 'diluent_info' in kw:
kw['diluent_info'] = 'generic_buffer'
return PlannedSampleDilution.get_entity(**kw)
def _create_planned_sample_dilution(self, **kw):
if not 'volume' in kw:
kw['volume'] = 0.000020
if not 'target_position' in kw:
kw['target_position'] = self._get_entity(IRackPosition)
if not 'diluent_info' in kw:
kw['diluent_info'] = 'generic_buffer'
return PlannedSampleDilution.get_entity(**kw)
def __create_buffer_worklist(self, sector_layout, buffer_volume, label):
# Creates the buffer dilution worklist for a particular quadrant
# and adds it to the worklist series.
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
ptfs = []
for rack_pos_96 in sector_layout.get_positions():
planned_transfer = PlannedSampleDilution.get_entity(volume, self.DILUTION_INFO, rack_pos_96)
ptfs.append(planned_transfer)
worklist = PlannedWorklist(
label, TRANSFER_TYPES.SAMPLE_DILUTION, get_pipetting_specs_biomek(), planned_liquid_transfers=ptfs
)
self.__worklist_series.add_worklist(self.__last_worklist_index, worklist)
self.__last_worklist_index += 1
def _create_planned_liquid_transfers(self):
"""
Generates the planned container dilution for the worklist.
"""
self.add_debug('Generate planned container dilutions ...')
for rack_pos, tf_pos in self.transfection_layout.iterpositions():
if tf_pos.is_empty: continue
volume = self.__determine_volume(tf_pos) / VOLUME_CONVERSION_FACTOR
target_position = rack_pos
psd = PlannedSampleDilution.get_entity(volume=volume,
target_position=target_position,
diluent_info=self.DILUENT_INFO)
self._add_planned_transfer(psd)
def _create_planned_liquid_transfers(self):
"""
Generates the planned container dilution for the worklist.
"""
self.add_debug('Generate planned container dilutions ...')
for rack_pos, tf_pos in self.transfection_layout.iterpositions():
if tf_pos.is_empty: continue
volume = self.__determine_volume(tf_pos) / VOLUME_CONVERSION_FACTOR
target_position = rack_pos
psd = PlannedSampleDilution.get_entity(
volume=volume,
target_position=target_position,
diluent_info=self.DILUENT_INFO)
self._add_planned_transfer(psd)
def _create_planned_liquid_transfers(self):
"""
Generates the planned container dilutions for the worklist.
"""
self.add_debug('Generate planned container dilutions ...')
volume = TransfectionParameters.TRANSFER_VOLUME * \
(TransfectionParameters.CELL_DILUTION_FACTOR - 1) \
/ VOLUME_CONVERSION_FACTOR
for tf_pos in self.transfection_layout.working_positions():
if tf_pos.is_empty:
continue
for target_pos in tf_pos.cell_plate_positions:
psd = PlannedSampleDilution.get_entity(volume=volume,
target_position=target_pos,
diluent_info=self.DILUENT_INFO)
self._add_planned_transfer(psd)
def _create_planned_liquid_transfers(self):
"""
Generates the planned container dilutions for the worklist.
"""
self.add_debug('Generate planned container dilutions ...')
volume = TransfectionParameters.TRANSFER_VOLUME * \
(TransfectionParameters.CELL_DILUTION_FACTOR - 1) \
/ VOLUME_CONVERSION_FACTOR
for tf_pos in self.transfection_layout.working_positions():
if tf_pos.is_empty:
continue
for target_pos in tf_pos.cell_plate_positions:
psd = PlannedSampleDilution.get_entity(
volume=volume,
target_position=target_pos,
diluent_info=self.DILUENT_INFO)
self._add_planned_transfer(psd)
def __create_buffer_worklist(self, sector_layout, buffer_volume, label):
# Creates the buffer dilution worklist for a particular quadrant
# and adds it to the worklist series.
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
ptfs = []
for rack_pos_96 in sector_layout.get_positions():
planned_transfer = PlannedSampleDilution.get_entity(
volume,
self.DILUTION_INFO,
rack_pos_96)
ptfs.append(planned_transfer)
worklist = PlannedWorklist(label,
TRANSFER_TYPES.SAMPLE_DILUTION,
get_pipetting_specs_biomek(),
planned_liquid_transfers=ptfs)
self.__worklist_series.add_worklist(self.__last_worklist_index,
worklist)
self.__last_worklist_index += 1
def __create_transfers(self):
# Creates a :class:`PlannedSampleDilution` for each rack position
# in a 8x12 rack shape.
self.add_debug('Create transfers ...')
self._run_and_record_error(self.volume_calculator.calculate,
'Error when trying to determine buffer volume: ',
ValueError)
buffer_volume = self.volume_calculator.get_buffer_volume()
if buffer_volume is not None:
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
wl_label = LABELS.create_buffer_worklist_label(
self.iso_request_label)
wl = PlannedWorklist(wl_label,
TRANSFER_TYPES.SAMPLE_DILUTION,
get_pipetting_specs_cybio())
for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
psd = PlannedSampleDilution.get_entity(volume=volume,
target_position=rack_pos, diluent_info=DILUENT_INFO)
wl.planned_liquid_transfers.append(psd)
self.__worklist_series.add_worklist(self.BUFFER_WORKLIST_INDEX, wl)
def __create_transfers(self):
# Creates a :class:`PlannedSampleDilution` for each rack position
# in a 8x12 rack shape.
self.add_debug('Create transfers ...')
self._run_and_record_error(
self.volume_calculator.calculate,
'Error when trying to determine buffer volume: ', ValueError)
buffer_volume = self.volume_calculator.get_buffer_volume()
if buffer_volume is not None:
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
wl_label = LABELS.create_buffer_worklist_label(
self.iso_request_label)
wl = PlannedWorklist(wl_label, TRANSFER_TYPES.SAMPLE_DILUTION,
get_pipetting_specs_cybio())
for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
psd = PlannedSampleDilution.get_entity(
volume=volume,
target_position=rack_pos,
diluent_info=DILUENT_INFO)
wl.planned_liquid_transfers.append(psd)
self.__worklist_series.add_worklist(self.BUFFER_WORKLIST_INDEX, wl)
def __create_buffer_worklist(self, quadrant_layout, buffer_volume, label,
sector_index):
# Creates buffer dilutions worklist for a particular quadrant
# and adds it to the worklist series.
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
planned_transfers = []
translator = RackSectorTranslator(
number_sectors=NUMBER_SECTORS,
source_sector_index=sector_index,
target_sector_index=0,
enforce_type=RackSectorTranslator.ONE_TO_MANY)
for rack_pos_384 in quadrant_layout.get_positions():
rack_pos_96 = translator.translate(rack_pos_384)
planned_transfer = PlannedSampleDilution.get_entity(
volume, self.DILUTION_INFO, rack_pos_96)
planned_transfers.append(planned_transfer)
worklist = PlannedWorklist(label=label,
planned_transfers=planned_transfers)
self.__last_worklist_index += 1
self.__worklist_series.add_worklist(self.__last_worklist_index,
worklist)